Is there a minimum efficiency for boilers that are being retrofitted?
I don't think there are rules on replacement boilers. In new construction it depends on which SB-12 Compliance Package the builder chooses. For example Package A1 requires space heating equipment with an AFUE of at least 96% and a water heater with at least a 0.8 Energy Factor. So I assume the boiler would need to have an EF of 0.8.
Check out pages 13 and 21 of the attached guide. Looks like 83% on commercial replacements.